7 files changed, 375 insertions, 111 deletions

diff --git a/Documentation/git-sparse-checkout.txt b/Documentation/git-sparse-checkout.txt
index c0342e5393..1a3ace6082 100644
--- a/Documentation/git-sparse-checkout.txt
+++ b/Documentation/git-sparse-checkout.txt
@@ -70,6 +70,16 @@ C-style quoted strings.
 	`core.sparseCheckoutCone` is enabled, the given patterns are interpreted
 	as directory names as in the 'set' subcommand.
 
+'reapply::
+	Reapply the sparsity pattern rules to paths in the working tree.
+	Commands like merge or rebase can materialize paths to do their
+	work (e.g. in order to show you a conflict), and other
+	sparse-checkout commands might fail to sparsify an individual file
+	(e.g. because it has unstaged changes or conflicts).  In such
+	cases, it can make sense to run `git sparse-checkout reapply` later
+	after cleaning up affected paths (e.g. resolving conflicts, undoing
+	or committing changes, etc.).
+
 'disable'::
 	Disable the `core.sparseCheckout` config setting, and restore the
 	working directory to include all files. Leaves the sparse-checkout
diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 740da4b6d5..95d0882417 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -18,7 +18,7 @@
 static const char *empty_base = "";
 
 static char const * const builtin_sparse_checkout_usage[] = {
-	N_("git sparse-checkout (init|list|set|add|disable) <options>"),
+	N_("git sparse-checkout (init|list|set|add|reapply|disable) <options>"),
 	NULL
 };
 
@@ -94,50 +94,37 @@ static int sparse_checkout_list(int argc, const char **argv)
 
 static int update_working_directory(struct pattern_list *pl)
 {
-	int result = 0;
+	enum update_sparsity_result result;
 	struct unpack_trees_options o;
 	struct lock_file lock_file = LOCK_INIT;
-	struct object_id oid;
-	struct tree *tree;
-	struct tree_desc t;
 	struct repository *r = the_repository;
 
-	if (repo_read_index_unmerged(r))
-		die(_("you need to resolve your current index first"));
-
-	if (get_oid("HEAD", &oid))
-		return 0;
-
-	tree = parse_tree_indirect(&oid);
-	parse_tree(tree);
-	init_tree_desc(&t, tree->buffer, tree->size);
-
 	memset(&o, 0, sizeof(o));
 	o.verbose_update = isatty(2);
-	o.merge = 1;
 	o.update = 1;
-	o.fn = oneway_merge;
 	o.head_idx = -1;
 	o.src_index = r->index;
 	o.dst_index = r->index;
 	o.skip_sparse_checkout = 0;
 	o.pl = pl;
-	o.keep_pattern_list = !!pl;
 
-	resolve_undo_clear_index(r->index);
 	setup_work_tree();
 
-	cache_tree_free(&r->index->cache_tree);
-
 	repo_hold_locked_index(r, &lock_file, LOCK_DIE_ON_ERROR);
 
-	core_apply_sparse_checkout = 1;
-	result = unpack_trees(1, &t, &o);
-
-	if (!result) {
-		prime_cache_tree(r, r->index, tree);
+	setup_unpack_trees_porcelain(&o, "sparse-checkout");
+	result = update_sparsity(&o);
+	clear_unpack_trees_porcelain(&o);
+
+	if (result == UPDATE_SPARSITY_WARNINGS)
+		/*
+		 * We don't do any special handling of warnings from untracked
+		 * files in the way or dirty entries that can't be removed.
+		 */
+		result = UPDATE_SPARSITY_SUCCESS;
+	if (result == UPDATE_SPARSITY_SUCCESS)
 		write_locked_index(r->index, &lock_file, COMMIT_LOCK);
-	} else
+	else
 		rollback_lock_file(&lock_file);
 
 	return result;
@@ -304,8 +291,6 @@ static int sparse_checkout_init(int argc, const char **argv)
 	};
 
 	repo_read_index(the_repository);
-	require_clean_work_tree(the_repository,
-				N_("initialize sparse-checkout"), NULL, 1, 0);
 
 	argc = parse_options(argc, argv, NULL,
 			     builtin_sparse_checkout_init_options,
@@ -560,8 +545,6 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 	};
 
 	repo_read_index(the_repository);
-	require_clean_work_tree(the_repository,
-				N_("set sparse-checkout patterns"), NULL, 1, 0);
 
 	argc = parse_options(argc, argv, prefix,
 			     builtin_sparse_checkout_set_options,
@@ -571,14 +554,18 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix,
 	return modify_pattern_list(argc, argv, m);
 }
 
+static int sparse_checkout_reapply(int argc, const char **argv)
+{
+	repo_read_index(the_repository);
+	return update_working_directory(NULL);
+}
+
 static int sparse_checkout_disable(int argc, const char **argv)
 {
 	struct pattern_list pl;
 	struct strbuf match_all = STRBUF_INIT;
 
 	repo_read_index(the_repository);
-	require_clean_work_tree(the_repository,
-				N_("disable sparse-checkout"), NULL, 1, 0);
 
 	memset(&pl, 0, sizeof(pl));
 	hashmap_init(&pl.recursive_hashmap, pl_hashmap_cmp, NULL, 0);
@@ -622,6 +609,8 @@ int cmd_sparse_checkout(int argc, const char **argv, const char *prefix)
 			return sparse_checkout_set(argc, argv, prefix, REPLACE);
 		if (!strcmp(argv[0], "add"))
 			return sparse_checkout_set(argc, argv, prefix, ADD);
+		if (!strcmp(argv[0], "reapply"))
+			return sparse_checkout_reapply(argc, argv);
 		if (!strcmp(argv[0], "disable"))
 			return sparse_checkout_disable(argc, argv);
 	}
diff --git a/t/t1011-read-tree-sparse-checkout.sh b/t/t1011-read-tree-sparse-checkout.sh
index eb44bafb59..63223e13bd 100755
--- a/t/t1011-read-tree-sparse-checkout.sh
+++ b/t/t1011-read-tree-sparse-checkout.sh
@@ -233,18 +233,19 @@ test_expect_success 'read-tree --reset removes outside worktree' '
 	test_must_be_empty result
 '
 
-test_expect_success 'print errors when failed to update worktree' '
+test_expect_success 'print warnings when some worktree updates disabled' '
 	echo sub >.git/info/sparse-checkout &&
 	git checkout -f init &&
 	mkdir sub &&
 	touch sub/added sub/addedtoo &&
-	test_must_fail git checkout top 2>actual &&
+	# Use -q to suppress "Previous HEAD position" and "Head is now at" msgs
+	git checkout -q top 2>actual &&
 	cat >expected <<\EOF &&
-error: The following untracked working tree files would be overwritten by checkout:
+warning: The following paths were already present and thus not updated despite sparse patterns:
 	sub/added
 	sub/addedtoo
-Please move or remove them before you switch branches.
-Aborting
+
+After fixing the above paths, you may want to run `git sparse-checkout reapply`.
 EOF
 	test_i18ncmp expected actual
 '
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index 44a91205d6..dee99eeec3 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -277,15 +277,23 @@ test_expect_success 'cone mode: add parent path' '
 	check_files repo a deep folder1
 '
 
-test_expect_success 'revert to old sparse-checkout on bad update' '
+test_expect_success 'not-up-to-date does not block rest of sparsification' '
+	test_when_finished git -C repo sparse-checkout disable &&
 	test_when_finished git -C repo reset --hard &&
 	git -C repo sparse-checkout set deep &&
+
 	echo update >repo/deep/deeper2/a &&
 	cp repo/.git/info/sparse-checkout expect &&
-	test_must_fail git -C repo sparse-checkout set deep/deeper1 2>err &&
-	test_i18ngrep "cannot set sparse-checkout patterns" err &&
-	test_cmp repo/.git/info/sparse-checkout expect &&
-	check_files repo/deep a deeper1 deeper2
+	test_write_lines "!/deep/*/" "/deep/deeper1/" >>expect &&
+
+	git -C repo sparse-checkout set deep/deeper1 2>err &&
+
+	test_i18ngrep "The following paths are not up to date" err &&
+	test_cmp expect repo/.git/info/sparse-checkout &&
+	check_files repo/deep a deeper1 deeper2 &&
+	check_files repo/deep/deeper1 a deepest &&
+	check_files repo/deep/deeper1/deepest a &&
+	check_files repo/deep/deeper2 a
 '
 
 test_expect_success 'revert to old sparse-checkout on empty update' '
@@ -315,19 +323,96 @@ test_expect_success '.gitignore should not warn about cone mode' '
 	test_i18ngrep ! "disabling cone patterns" err
 '
 
-test_expect_success 'sparse-checkout (init|set|disable) fails with dirty status' '
+test_expect_success 'sparse-checkout (init|set|disable) warns with dirty status' '
 	git clone repo dirty &&
 	echo dirty >dirty/folder1/a &&
-	test_must_fail git -C dirty sparse-checkout init &&
-	test_must_fail git -C dirty sparse-checkout set /folder2/* /deep/deeper1/* &&
-	test_must_fail git -C dirty sparse-checkout disable &&
+
+	git -C dirty sparse-checkout init 2>err &&
+	test_i18ngrep "warning.*The following paths are not up to date" err &&
+
+	git -C dirty sparse-checkout set /folder2/* /deep/deeper1/* 2>err &&
+	test_i18ngrep "warning.*The following paths are not up to date" err &&
+	test_path_is_file dirty/folder1/a &&
+
+	git -C dirty sparse-checkout disable 2>err &&
+	test_must_be_empty err &&
+
 	git -C dirty reset --hard &&
 	git -C dirty sparse-checkout init &&
 	git -C dirty sparse-checkout set /folder2/* /deep/deeper1/* &&
-	git -C dirty sparse-checkout disable
+	test_path_is_missing dirty/folder1/a &&
+	git -C dirty sparse-checkout disable &&
+	test_path_is_file dirty/folder1/a
+'
+
+test_expect_success 'sparse-checkout (init|set|disable) warns with unmerged status' '
+	git clone repo unmerged &&
+
+	cat >input <<-EOF &&
+	0 0000000000000000000000000000000000000000	folder1/a
+	100644 $(git -C unmerged rev-parse HEAD:folder1/a) 1	folder1/a
+	EOF
+	git -C unmerged update-index --index-info <input &&
+
+	git -C unmerged sparse-checkout init 2>err &&
+	test_i18ngrep "warning.*The following paths are unmerged" err &&
+
+	git -C unmerged sparse-checkout set /folder2/* /deep/deeper1/* 2>err &&
+	test_i18ngrep "warning.*The following paths are unmerged" err &&
+	test_path_is_file dirty/folder1/a &&
+
+	git -C unmerged sparse-checkout disable 2>err &&
+	test_i18ngrep "warning.*The following paths are unmerged" err &&
+
+	git -C unmerged reset --hard &&
+	git -C unmerged sparse-checkout init &&
+	git -C unmerged sparse-checkout set /folder2/* /deep/deeper1/* &&
+	git -C unmerged sparse-checkout disable
+'
+
+test_expect_success 'sparse-checkout reapply' '
+	git clone repo tweak &&
+
+	echo dirty >tweak/deep/deeper2/a &&
+
+	cat >input <<-EOF &&
+	0 0000000000000000000000000000000000000000	folder1/a
+	100644 $(git -C tweak rev-parse HEAD:folder1/a) 1	folder1/a
+	EOF
+	git -C tweak update-index --index-info <input &&
+
+	git -C tweak sparse-checkout init --cone 2>err &&
+	test_i18ngrep "warning.*The following paths are not up to date" err &&
+	test_i18ngrep "warning.*The following paths are unmerged" err &&
+
+	git -C tweak sparse-checkout set folder2 deep/deeper1 2>err &&
+	test_i18ngrep "warning.*The following paths are not up to date" err &&
+	test_i18ngrep "warning.*The following paths are unmerged" err &&
+
+	git -C tweak sparse-checkout reapply 2>err &&
+	test_i18ngrep "warning.*The following paths are not up to date" err &&
+	test_path_is_file tweak/deep/deeper2/a &&
+	test_i18ngrep "warning.*The following paths are unmerged" err &&
+	test_path_is_file tweak/folder1/a &&
+
+	git -C tweak checkout HEAD deep/deeper2/a &&
+	git -C tweak sparse-checkout reapply 2>err &&
+	test_i18ngrep ! "warning.*The following paths are not up to date" err &&
+	test_path_is_missing tweak/deep/deeper2/a &&
+	test_i18ngrep "warning.*The following paths are unmerged" err &&
+	test_path_is_file tweak/folder1/a &&
+
+	git -C tweak add folder1/a &&
+	git -C tweak sparse-checkout reapply 2>err &&
+	test_must_be_empty err &&
+	test_path_is_missing tweak/deep/deeper2/a &&
+	test_path_is_missing tweak/folder1/a &&
+
+	git -C tweak sparse-checkout disable
 '
 
 test_expect_success 'cone mode: set with core.ignoreCase=true' '
+	rm repo/.git/info/sparse-checkout &&
 	git -C repo sparse-checkout init --cone &&
 	git -C repo -c core.ignoreCase=true sparse-checkout set folder1 &&
 	cat >expect <<-\EOF &&
diff --git a/t/t2018-checkout-branch.sh b/t/t2018-checkout-branch.sh
index bbca7ef8da..21583154d8 100755
--- a/t/t2018-checkout-branch.sh
+++ b/t/t2018-checkout-branch.sh
@@ -238,4 +238,26 @@ test_expect_success 'checkout -b after clone --no-checkout does a checkout of HE
 	test_path_is_file dest/a.t
 '
 
+test_expect_success 'checkout -b to a new branch preserves mergeable changes despite sparse-checkout' '
+	test_when_finished "
+		git reset --hard &&
+		git checkout branch1-scratch &&
+		test_might_fail git branch -D branch3 &&
+		git config core.sparseCheckout false &&
+		rm .git/info/sparse-checkout" &&
+
+	test_commit file2 &&
+
+	echo stuff >>file1 &&
+	echo file2 >.git/info/sparse-checkout &&
+	git config core.sparseCheckout true &&
+
+	CURHEAD=$(git rev-parse HEAD) &&
+	do_checkout branch3 $CURHEAD &&
+
+	echo file1 >expect &&
+	git diff --name-only >actual &&
+	test_cmp expect actual
+'
+
 test_done
diff --git a/unpack-trees.c b/unpack-trees.c
index 4c3191b947..6bbf58d28e 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -24,7 +24,7 @@
  * situation better.  See how "git checkout" and "git merge" replaces
  * them using setup_unpack_trees_porcelain(), for example.
  */
-static const char *unpack_plumbing_errors[NB_UNPACK_TREES_ERROR_TYPES] = {
+static const char *unpack_plumbing_errors[NB_UNPACK_TREES_WARNING_TYPES] = {
 	/* ERROR_WOULD_OVERWRITE */
 	"Entry '%s' would be overwritten by merge. Cannot merge.",
 
@@ -43,17 +43,20 @@ static const char *unpack_plumbing_errors[NB_UNPACK_TREES_ERROR_TYPES] = {
 	/* ERROR_BIND_OVERLAP */
 	"Entry '%s' overlaps with '%s'.  Cannot bind.",
 
-	/* ERROR_SPARSE_NOT_UPTODATE_FILE */
-	"Entry '%s' not uptodate. Cannot update sparse checkout.",
+	/* ERROR_WOULD_LOSE_SUBMODULE */
+	"Submodule '%s' cannot checkout new HEAD.",
 
-	/* ERROR_WOULD_LOSE_ORPHANED_OVERWRITTEN */
-	"Working tree file '%s' would be overwritten by sparse checkout update.",
+	/* NB_UNPACK_TREES_ERROR_TYPES; just a meta value */
+	"",
 
-	/* ERROR_WOULD_LOSE_ORPHANED_REMOVED */
-	"Working tree file '%s' would be removed by sparse checkout update.",
+	/* WARNING_SPARSE_NOT_UPTODATE_FILE */
+	"Path '%s' not uptodate; will not remove from working tree.",
 
-	/* ERROR_WOULD_LOSE_SUBMODULE */
-	"Submodule '%s' cannot checkout new HEAD.",
+	/* WARNING_SPARSE_UNMERGED_FILE */
+	"Path '%s' unmerged; will not remove from working tree.",
+
+	/* WARNING_SPARSE_ORPHANED_NOT_OVERWRITTEN */
+	"Path '%s' already present; will not overwrite with sparse update.",
 };
 
 #define ERRORMSG(o,type) \
@@ -168,15 +171,16 @@ void setup_unpack_trees_porcelain(struct unpack_trees_options *opts,
 	 */
 	msgs[ERROR_BIND_OVERLAP] = _("Entry '%s' overlaps with '%s'.  Cannot bind.");
 
-	msgs[ERROR_SPARSE_NOT_UPTODATE_FILE] =
-		_("Cannot update sparse checkout: the following entries are not up to date:\n%s");
-	msgs[ERROR_WOULD_LOSE_ORPHANED_OVERWRITTEN] =
-		_("The following working tree files would be overwritten by sparse checkout update:\n%s");
-	msgs[ERROR_WOULD_LOSE_ORPHANED_REMOVED] =
-		_("The following working tree files would be removed by sparse checkout update:\n%s");
 	msgs[ERROR_WOULD_LOSE_SUBMODULE] =
 		_("Cannot update submodule:\n%s");
 
+	msgs[WARNING_SPARSE_NOT_UPTODATE_FILE] =
+		_("The following paths are not up to date and were left despite sparse patterns:\n%s");
+	msgs[WARNING_SPARSE_UNMERGED_FILE] =
+		_("The following paths are unmerged and were left despite sparse patterns:\n%s");
+	msgs[WARNING_SPARSE_ORPHANED_NOT_OVERWRITTEN] =
+		_("The following paths were already present and thus not updated despite sparse patterns:\n%s");
+
 	opts->show_all_errors = 1;
 	/* rejected paths may not have a static buffer */
 	for (i = 0; i < ARRAY_SIZE(opts->unpack_rejects); i++)
@@ -226,7 +230,7 @@ static int add_rejected_path(struct unpack_trees_options *o,
 
 	/*
 	 * Otherwise, insert in a list for future display by
-	 * display_error_msgs()
+	 * display_(error|warning)_msgs()
 	 */
 	string_list_append(&o->unpack_rejects[e], path);
 	return -1;
@@ -237,13 +241,16 @@ static int add_rejected_path(struct unpack_trees_options *o,
  */
 static void display_error_msgs(struct unpack_trees_options *o)
 {
-	int e, i;
-	int something_displayed = 0;
+	int e;
+	unsigned error_displayed = 0;
 	for (e = 0; e < NB_UNPACK_TREES_ERROR_TYPES; e++) {
 		struct string_list *rejects = &o->unpack_rejects[e];
+
 		if (rejects->nr > 0) {
+			int i;
 			struct strbuf path = STRBUF_INIT;
-			something_displayed = 1;
+
+			error_displayed = 1;
 			for (i = 0; i < rejects->nr; i++)
 				strbuf_addf(&path, "\t%s\n", rejects->items[i].string);
 			error(ERRORMSG(o, e), super_prefixed(path.buf));
@@ -251,10 +258,36 @@ static void display_error_msgs(struct unpack_trees_options *o)
 		}
 		string_list_clear(rejects, 0);
 	}
-	if (something_displayed)
+	if (error_displayed)
 		fprintf(stderr, _("Aborting\n"));
 }
 
+/*
+ * display all the warning messages stored in a nice way
+ */
+static void display_warning_msgs(struct unpack_trees_options *o)
+{
+	int e;
+	unsigned warning_displayed = 0;
+	for (e = NB_UNPACK_TREES_ERROR_TYPES + 1;
+	     e < NB_UNPACK_TREES_WARNING_TYPES; e++) {
+		struct string_list *rejects = &o->unpack_rejects[e];
+
+		if (rejects->nr > 0) {
+			int i;
+			struct strbuf path = STRBUF_INIT;
+
+			warning_displayed = 1;
+			for (i = 0; i < rejects->nr; i++)
+				strbuf_addf(&path, "\t%s\n", rejects->items[i].string);
+			warning(ERRORMSG(o, e), super_prefixed(path.buf));
+			strbuf_release(&path);
+		}
+		string_list_clear(rejects, 0);
+	}
+	if (warning_displayed)
+		fprintf(stderr, _("After fixing the above paths, you may want to run `git sparse-checkout reapply`.\n"));
+}
 static int check_submodule_move_head(const struct cache_entry *ce,
 				     const char *old_id,
 				     const char *new_id,
@@ -357,12 +390,12 @@ static void report_collided_checkout(struct index_state *index)
 	string_list_clear(&list, 0);
 }
 
-static int check_updates(struct unpack_trees_options *o)
+static int check_updates(struct unpack_trees_options *o,
+			 struct index_state *index)
 {
 	unsigned cnt = 0;
 	int errs = 0;
 	struct progress *progress;
-	struct index_state *index = &o->result;
 	struct checkout state = CHECKOUT_INIT;
 	int i;
 
@@ -504,19 +537,39 @@ static int apply_sparse_checkout(struct index_state *istate,
 		 * also stat info may have lost after merged_entry() so calling
 		 * verify_uptodate() again may fail
 		 */
-		if (!(ce->ce_flags & CE_UPDATE) && verify_uptodate_sparse(ce, o))
+		if (!(ce->ce_flags & CE_UPDATE) &&
+		    verify_uptodate_sparse(ce, o)) {
+			ce->ce_flags &= ~CE_SKIP_WORKTREE;
 			return -1;
+		}
 		ce->ce_flags |= CE_WT_REMOVE;
 		ce->ce_flags &= ~CE_UPDATE;
 	}
 	if (was_skip_worktree && !ce_skip_worktree(ce)) {
-		if (verify_absent_sparse(ce, ERROR_WOULD_LOSE_UNTRACKED_OVERWRITTEN, o))
+		if (verify_absent_sparse(ce, WARNING_SPARSE_ORPHANED_NOT_OVERWRITTEN, o))
 			return -1;
 		ce->ce_flags |= CE_UPDATE;
 	}
 	return 0;
 }
 
+static int warn_conflicted_path(struct index_state *istate,
+				int i,
+				struct unpack_trees_options *o)
+{
+	char *conflicting_path = istate->cache[i]->name;
+	int count = 0;
+
+	add_rejected_path(o, WARNING_SPARSE_UNMERGED_FILE, conflicting_path);
+
+	/* Find out how many higher stage entries at same path */
+	while (++count < istate->cache_nr &&
+	       !strcmp(conflicting_path,
+		       istate->cache[i+count]->name))
+		/* do nothing */;
+	return count;
+}
+
 static inline int call_unpack_fn(const struct cache_entry * const *src,
 				 struct unpack_trees_options *o)
 {
@@ -1493,6 +1546,20 @@ static void mark_new_skip_worktree(struct pattern_list *pl,
 	clear_ce_flags(istate, select_flag, skip_wt_flag, pl, show_progress);
 }
 
+static void populate_from_existing_patterns(struct unpack_trees_options *o,
+					    struct pattern_list *pl)
+{
+	char *sparse = git_pathdup("info/sparse-checkout");
+
+	pl->use_cone_patterns = core_sparse_checkout_cone;
+	if (add_patterns_from_file_to_list(sparse, "", 0, pl, NULL) < 0)
+		o->skip_sparse_checkout = 1;
+	else
+		o->pl = pl;
+	free(sparse);
+}
+
+
 static int verify_absent(const struct cache_entry *,
 			 enum unpack_trees_error_types,
 			 struct unpack_trees_options *);
@@ -1507,22 +1574,18 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 	int i, ret;
 	static struct cache_entry *dfc;
 	struct pattern_list pl;
+	int free_pattern_list = 0;
 
 	if (len > MAX_UNPACK_TREES)
 		die("unpack_trees takes at most %d trees", MAX_UNPACK_TREES);
 
 	trace_performance_enter();
-	memset(&pl, 0, sizeof(pl));
 	if (!core_apply_sparse_checkout || !o->update)
 		o->skip_sparse_checkout = 1;
 	if (!o->skip_sparse_checkout && !o->pl) {
-		char *sparse = git_pathdup("info/sparse-checkout");
-		pl.use_cone_patterns = core_sparse_checkout_cone;
-		if (add_patterns_from_file_to_list(sparse, "", 0, &pl, NULL) < 0)
-			o->skip_sparse_checkout = 1;
-		else
-			o->pl = &pl;
-		free(sparse);
+		memset(&pl, 0, sizeof(pl));
+		free_pattern_list = 1;
+		populate_from_existing_patterns(o, &pl);
 	}
 
 	memset(&o->result, 0, sizeof(o->result));
@@ -1618,7 +1681,7 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 
 		/*
 		 * Sparse checkout loop #2: set NEW_SKIP_WORKTREE on entries not in loop #1
-		 * If the will have NEW_SKIP_WORKTREE, also set CE_SKIP_WORKTREE
+		 * If they will have NEW_SKIP_WORKTREE, also set CE_SKIP_WORKTREE
 		 * so apply_sparse_checkout() won't attempt to remove it from worktree
 		 */
 		mark_new_skip_worktree(o->pl, &o->result,
@@ -1638,23 +1701,15 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 			 * correct CE_NEW_SKIP_WORKTREE
 			 */
 			if (ce->ce_flags & CE_ADDED &&
-			    verify_absent(ce, ERROR_WOULD_LOSE_UNTRACKED_OVERWRITTEN, o)) {
-				if (!o->show_all_errors)
-					goto return_failed;
-				ret = -1;
-			}
+			    verify_absent(ce, WARNING_SPARSE_ORPHANED_NOT_OVERWRITTEN, o))
+				ret = 1;
+
+			if (apply_sparse_checkout(&o->result, ce, o))
+				ret = 1;
 
-			if (apply_sparse_checkout(&o->result, ce, o)) {
-				if (!o->show_all_errors)
-					goto return_failed;
-				ret = -1;
-			}
 			if (!ce_skip_worktree(ce))
 				empty_worktree = 0;
-
 		}
-		if (ret < 0)
-			goto return_failed;
 		/*
 		 * Sparse checkout is meant to narrow down checkout area
 		 * but it does not make sense to narrow down to empty working
@@ -1665,9 +1720,18 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 			ret = unpack_failed(o, "Sparse checkout leaves no entry on working directory");
 			goto done;
 		}
+		if (ret == 1) {
+			/*
+			 * Inability to sparsify or de-sparsify individual
+			 * paths is not an error, but just a warning.
+			 */
+			if (o->show_all_errors)
+				display_warning_msgs(o);
+			ret = 0;
+		}
 	}
 
-	ret = check_updates(o) ? (-2) : 0;
+	ret = check_updates(o, &o->result) ? (-2) : 0;
 	if (o->dst_index) {
 		move_index_extensions(&o->result, o->src_index);
 		if (!ret) {
@@ -1690,9 +1754,9 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 	o->src_index = NULL;
 
 done:
-	trace_performance_leave("unpack_trees");
-	if (!o->keep_pattern_list)
+	if (free_pattern_list)
 		clear_pattern_list(&pl);
+	trace_performance_leave("unpack_trees");
 	return ret;
 
 return_failed:
@@ -1705,6 +1769,91 @@ return_failed:
 	goto done;
 }
 
+/*
+ * Update SKIP_WORKTREE bits according to sparsity patterns, and update
+ * working directory to match.
+ *
+ * CE_NEW_SKIP_WORKTREE is used internally.
+ */
+enum update_sparsity_result update_sparsity(struct unpack_trees_options *o)
+{
+	enum update_sparsity_result ret = UPDATE_SPARSITY_SUCCESS;
+	struct pattern_list pl;
+	int i, empty_worktree;
+	unsigned old_show_all_errors;
+	int free_pattern_list = 0;
+
+	old_show_all_errors = o->show_all_errors;
+	o->show_all_errors = 1;
+
+	/* Sanity checks */
+	if (!o->update || o->index_only || o->skip_sparse_checkout)
+		BUG("update_sparsity() is for reflecting sparsity patterns in working directory");
+	if (o->src_index != o->dst_index || o->fn)
+		BUG("update_sparsity() called wrong");
+
+	trace_performance_enter();
+
+	/* If we weren't given patterns, use the recorded ones */
+	if (!o->pl) {
+		memset(&pl, 0, sizeof(pl));
+		free_pattern_list = 1;
+		populate_from_existing_patterns(o, &pl);
+		if (o->skip_sparse_checkout)
+			goto skip_sparse_checkout;
+	}
+
+	/* Set NEW_SKIP_WORKTREE on existing entries. */
+	mark_all_ce_unused(o->src_index);
+	mark_new_skip_worktree(o->pl, o->src_index, 0,
+			       CE_NEW_SKIP_WORKTREE, o->verbose_update);
+
+	/* Then loop over entries and update/remove as needed */
+	ret = UPDATE_SPARSITY_SUCCESS;
+	empty_worktree = 1;
+	for (i = 0; i < o->src_index->cache_nr; i++) {
+		struct cache_entry *ce = o->src_index->cache[i];
+
+
+		if (ce_stage(ce)) {
+			/* -1 because for loop will increment by 1 */
+			i += warn_conflicted_path(o->src_index, i, o) - 1;
+			ret = UPDATE_SPARSITY_WARNINGS;
+			continue;
+		}
+
+		if (apply_sparse_checkout(o->src_index, ce, o))
+			ret = UPDATE_SPARSITY_WARNINGS;
+
+		if (!ce_skip_worktree(ce))
+			empty_worktree = 0;
+	}
+
+	/*
+	 * Sparse checkout is meant to narrow down checkout area
+	 * but it does not make sense to narrow down to empty working
+	 * tree. This is usually a mistake in sparse checkout rules.
+	 * Do not allow users to do that.
+	 */
+	if (o->src_index->cache_nr && empty_worktree) {
+		unpack_failed(o, "Sparse checkout leaves no entry on working directory");
+		ret = UPDATE_SPARSITY_INDEX_UPDATE_FAILURES;
+		goto done;
+	}
+
+skip_sparse_checkout:
+	if (check_updates(o, o->src_index))
+		ret = UPDATE_SPARSITY_WORKTREE_UPDATE_FAILURES;
+
+done:
+	display_warning_msgs(o);
+	o->show_all_errors = old_show_all_errors;
+	if (free_pattern_list)
+		clear_pattern_list(&pl);
+	trace_performance_leave("update_sparsity");
+	return ret;
+}
+
 /* Here come the merge functions */
 
 static int reject_merge(const struct cache_entry *ce,
@@ -1789,7 +1938,7 @@ int verify_uptodate(const struct cache_entry *ce,
 static int verify_uptodate_sparse(const struct cache_entry *ce,
 				  struct unpack_trees_options *o)
 {
-	return verify_uptodate_1(ce, o, ERROR_SPARSE_NOT_UPTODATE_FILE);
+	return verify_uptodate_1(ce, o, WARNING_SPARSE_NOT_UPTODATE_FILE);
 }
 
 /*
@@ -2027,11 +2176,7 @@ static int verify_absent_sparse(const struct cache_entry *ce,
 				enum unpack_trees_error_types error_type,
 				struct unpack_trees_options *o)
 {
-	enum unpack_trees_error_types orphaned_error = error_type;
-	if (orphaned_error == ERROR_WOULD_LOSE_UNTRACKED_OVERWRITTEN)
-		orphaned_error = ERROR_WOULD_LOSE_ORPHANED_OVERWRITTEN;
-
-	return verify_absent_1(ce, orphaned_error, o);
+	return verify_absent_1(ce, error_type, o);
 }
 
 static int merged_entry(const struct cache_entry *ce,
diff --git a/unpack-trees.h b/unpack-trees.h
index ad41b45a71..9c2f08277e 100644
--- a/unpack-trees.h
+++ b/unpack-trees.h
@@ -22,11 +22,15 @@ enum unpack_trees_error_types {
 	ERROR_WOULD_LOSE_UNTRACKED_OVERWRITTEN,
 	ERROR_WOULD_LOSE_UNTRACKED_REMOVED,
 	ERROR_BIND_OVERLAP,
-	ERROR_SPARSE_NOT_UPTODATE_FILE,
-	ERROR_WOULD_LOSE_ORPHANED_OVERWRITTEN,
-	ERROR_WOULD_LOSE_ORPHANED_REMOVED,
 	ERROR_WOULD_LOSE_SUBMODULE,
-	NB_UNPACK_TREES_ERROR_TYPES
+
+	NB_UNPACK_TREES_ERROR_TYPES,
+
+	WARNING_SPARSE_NOT_UPTODATE_FILE,
+	WARNING_SPARSE_UNMERGED_FILE,
+	WARNING_SPARSE_ORPHANED_NOT_OVERWRITTEN,
+
+	NB_UNPACK_TREES_WARNING_TYPES,
 };
 
 /*
@@ -59,20 +63,19 @@ struct unpack_trees_options {
 		     quiet,
 		     exiting_early,
 		     show_all_errors,
-		     dry_run,
-		     keep_pattern_list;
+		     dry_run;
 	const char *prefix;
 	int cache_bottom;
 	struct dir_struct *dir;
 	struct pathspec *pathspec;
 	merge_fn_t fn;
-	const char *msgs[NB_UNPACK_TREES_ERROR_TYPES];
+	const char *msgs[NB_UNPACK_TREES_WARNING_TYPES];
 	struct argv_array msgs_to_free;
 	/*
 	 * Store error messages in an array, each case
 	 * corresponding to a error message type
 	 */
-	struct string_list unpack_rejects[NB_UNPACK_TREES_ERROR_TYPES];
+	struct string_list unpack_rejects[NB_UNPACK_TREES_WARNING_TYPES];
 
 	int head_idx;
 	int merge_size;
@@ -91,6 +94,15 @@ struct unpack_trees_options {
 int unpack_trees(unsigned n, struct tree_desc *t,
 		 struct unpack_trees_options *options);
 
+enum update_sparsity_result {
+	UPDATE_SPARSITY_SUCCESS = 0,
+	UPDATE_SPARSITY_WARNINGS = 1,
+	UPDATE_SPARSITY_INDEX_UPDATE_FAILURES = -1,
+	UPDATE_SPARSITY_WORKTREE_UPDATE_FAILURES = -2
+};
+
+enum update_sparsity_result update_sparsity(struct unpack_trees_options *options);
+
 int verify_uptodate(const struct cache_entry *ce,
 		    struct unpack_trees_options *o);